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Detailed information for vg1206392661:

Variant ID: vg1206392661 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 6392661
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.91, T: 0.08, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:

CCGGGAGCGGTTCAGCGGGCTGCGCGCGCCGGCGTGGCTGCTGCTGCCCTGCTCGACCACCTCGTCGCCGTTGTTCGTCGAGCATCCGGTCCGTGGACTC[C/T]
ACCAAAACTCAAATGATAGAACAAAACCATCAGATAGATTAACAGGTAAAAGCACAAAATCATCAGTCTTAGGGCGCACGGCGACCCGGCGTCTATGCCA

Reverse complement sequence

TGGCATAGACGCCGGGTCGCCGTGCGCCCTAAGACTGATGATTTTGTGCTTTTACCTGTTAATCTATCTGATGGTTTTGTTCTATCATTTGAGTTTTGGT[G/A]
GAGTCCACGGACCGGATGCTCGACGAACAACGGCGACGAGGTGGTCGAGCAGGGCAGCAGCAGCCACGCCGGCGCGCGCAGCCCGCTGAACCGCTCCCGG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	24.50%	17.20%	0.23%	57.98%	NA
All Indica	2759	35.30%	3.90%	0.29%	60.49%	NA
All Japonica	1512	5.60%	38.60%	0.07%	55.75%	NA
Aus	269	2.20%	36.10%	0.37%	61.34%	NA
Indica I	595	85.70%	6.20%	0.00%	8.07%	NA
Indica II	465	18.70%	2.20%	0.43%	78.71%	NA
Indica III	913	10.80%	2.80%	0.44%	85.87%	NA
Indica Intermediate	786	35.40%	4.50%	0.25%	59.92%	NA
Temperate Japonica	767	9.60%	45.20%	0.13%	44.98%	NA
Tropical Japonica	504	1.00%	22.40%	0.00%	76.59%	NA
Japonica Intermediate	241	2.50%	51.00%	0.00%	46.47%	NA
VI/Aromatic	96	68.80%	10.40%	0.00%	20.83%	NA
Intermediate	90	32.20%	18.90%	1.11%	47.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1206392661	C -> DEL	N	N	silent_mutation	Average:66.372; most accessible tissue: Zhenshan97 flag leaf, score: 79.247	N	N	N	N
vg1206392661	C -> T	LOC_Os12g11780.1	upstream_gene_variant ; 717.0bp to feature; MODIFIER	silent_mutation	Average:66.372; most accessible tissue: Zhenshan97 flag leaf, score: 79.247	N	N	N	N
vg1206392661	C -> T	LOC_Os12g11790.1	downstream_gene_variant ; 255.0bp to feature; MODIFIER	silent_mutation	Average:66.372; most accessible tissue: Zhenshan97 flag leaf, score: 79.247	N	N	N	N
vg1206392661	C -> T	LOC_Os12g11780-LOC_Os12g11790	intergenic_region ; MODIFIER	silent_mutation	Average:66.372; most accessible tissue: Zhenshan97 flag leaf, score: 79.247	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1206392661	5.01E-06	5.01E-06	mr1582	All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251